Wdlupdate (#6)

* added cram-to-bam. updated pairedtoubam to use gatk4

* Update README.md

removed gatk software requiremnt because repo will contain more than one wdl which may use different versions.

* Update README.md

* Wdl now uses a readgroup tsv file as input. Added task to compose a file containing a list of the generated ubams

* minor

* minor

* minor edits

* corrected memory placement

* minor edits

* added bam-to-unmapped-bams wdl

* fixed comment number

* changed to use latest gatk docker

* fastq to bam now uses arrays as input

* updated descriptor for paired fastq to bam

* updated inpute in description

* added a firecloud version for fastq to Ubam

* minor format changes. chaged pairedfastq2Ubam docker to gcr

* Minor update to ReadMe, added default docker to cram2bam

* decreased mem size in cram2bam to reduce cost

README.md

@@ -43,6 +43,15 @@ This WDL converts BAM  to unmapped BAMs
 #### Outputs 
 - Sorted Unmapped BAMs
 
+### interleaved-fastq-to-paired-fastq :
+This WDL takes in a single interleaved(R1+R2) FASTQ file and separates it into separate R1 and R2 FASTQ (i.e. paired FASTQ) files. Paired FASTQ files are the input format for the tool that generates unmapped BAMs (the format used in most GATK processing and analysis tools).
+
+#### Requirements/expectations 
+- Interleaved Fastq file
+
+#### Outputs 
+- Separate R1 and R2 FASTQ files (i.e. paired FASTQ)
+
 ### Software version requirements :
 - GATK4 or later
 - Samtools 1.3.1

cram-to-bam.inputs.json

@@ -16,8 +16,8 @@
   "CramToBamFlow.cram_to_bam_disk_size": "200",
 
   "##_COMMENT3": "MEMORY",
-  "CramToBamFlow.validate_sam_file_mem_size": "3500 MB",
-  "CramToBamFlow.cram_to_bam_mem_size": "15 GB",
+  "CramToBamFlow.validate_sam_file_mem_size": "3750 MB",
+  "CramToBamFlow.cram_to_bam_mem_size": "3.75 GB",
 
   "##_COMMENT3": "PREEMPTIBLES",
   "CramToBamFlow.ValidateSamFile.preemptible_tries": "3"

interleaved-fastq-to-paired-fastq.inputs.json

@@ -0,0 +1,7 @@
+{
+  "#UninterleaveFastqs.uninterleave_fqs.cpu": "Int? (optional)",
+  "#UninterleaveFastqs.uninterleave_fqs.memory": "Int? (optional)",
+  "#UninterleaveFastqs.uninterleave_fqs.disk": "Int? (optional)",
+  "UninterleaveFastqs.uninterleave_fqs.inputFastq": "gs://gatk-test-data/wgs_fastq/NA12878_20k/H06JUADXX130110.1.ATCACGAT.20k_interleaved.fastq"
+}
+

interleaved-fastq-to-paired-fastq.wdl

@@ -0,0 +1,44 @@
+#This WDL takes in a single interleaved(R1+R2) FASTQ file and separates it into separate R1 and R2 FASTQ (i.e. paired FASTQ) files. Paired FASTQ files are the input format for the tool that generates unmapped BAMs (the format used in most GATK processing and analysis tools).
+#
+#Requirements/expectations 
+#- Interleaved Fastq file
+#
+#Outputs 
+#- Separate R1 and R2 FASTQ files (i.e. paired FASTQ)
+#
+##################
+
+workflow UninterleaveFastqs {
+
+  call uninterleave_fqs
+}
+  task uninterleave_fqs {
+
+    File inputFastq
+
+    Int? cpu
+    Int? memory
+    Int? disk
+
+    String r1_name = basename(inputFastq, ".fastq") + "_reads_1.fastq"
+    String r2_name = basename(inputFastq, ".fastq") + "_reads_2.fastq"
+
+  command {
+    cat ${inputFastq} | paste - - - - - - - -  | \
+    tee >(cut -f 1-4 | tr "\t" "\n" > ${r1_name}) | \
+    cut -f 5-8 | tr "\t" "\n" > ${r2_name}
+  }
+
+  runtime {
+    docker: "ubuntu:latest"
+    memory: select_first([memory, 8]) + " GB"
+    cpu: select_first([cpu, 2])
+    zones: "us-central1-c us-central1-b"
+    disks: "local-disk " + select_first([disk, 3]) + " HDD"
+  }
+
+  output {
+    File r1_fastq = "${r1_name}"
+    File r2_fastq = "${r2_name}"
+  }
+}